Crystal structure of avidin - 6-(6-biotinamidohexanamido) hexanoylferrocene complex

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).

Ligands and binding sites

• B6F · [(1,2,3,4,5-eta)-cyclopentadienyl][(1,2,3,4,5-eta)-{6-[(6-{[5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanoyl]amino}hexanoyl)amino]hexanoyl}cyclopentadienyl]iron · ligand · 2 copies · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 156 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

• 4JHQ · Crystal structure of avidin - 6-(6-biotinamidohexanamido)hexanoylferrocene complex · the same entry in another collection · chain A against A, TM-score 1.00
• P02701 · AlphaFold monomer V2.0 prediction for avidin (P02701) · a predicted model of the same protein · chain A against A, TM-score 0.96

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P02701
• Elsewhere: RCSB PDB 4JHQ · PDBe 4JHQ · UniProt P02701